The team are called to help a rescue mission for xenobiologist Alexander Preloran, who disappeared while on a mission to explore the Leviathan, an alien spacecraft buried at the bottom of the Pacific Ocean for 65 million years.

As the aliens and their mutation allies attack Earth, H.E.A.T. escapes captivity. They battle to defeat the alien onslaught and free the mutations from their control to help humanity fight back and save the planet from conquest.